Align gamma-glutamylputrescine oxidase (EC 1.4.3.-) (characterized)
to candidate BPHYT_RS23125 BPHYT_RS23125 FAD-dependent oxidoreductase
Query= reanno::pseudo5_N2C3_1:AO356_21495 (427 letters) >FitnessBrowser__BFirm:BPHYT_RS23125 Length = 430 Score = 360 bits (924), Expect = e-104 Identities = 193/425 (45%), Positives = 261/425 (61%), Gaps = 4/425 (0%) Query: 2 ANTPYPESYYAASANPVPPRPALQDDVETDVCVIGAGYTGLSSALFLLENGFKVTVLEAA 61 +N P+ SYYAA+AN PAL + + DVCVIGAG TG+S+AL L E G V VLEA+ Sbjct: 5 SNQPHVASYYAATANDSTRHPALDETISVDVCVIGAGLTGISTALNLAERGHSVAVLEAS 64 Query: 62 KVGFGASGRNGGQIVNSYSRDIDVIERSVGPQQAQLLGNMAFEGGRIIRERVAKYQIQCD 121 KVG+ ASGRNGGQ++ ++ DID + + + + +M E I++ERVAK+QI CD Sbjct: 65 KVGWAASGRNGGQLIGGFACDIDTFAKYLPADDVKRVWDMGIETLDIVKERVAKHQIDCD 124 Query: 122 LKDGGVFAALTAKQMGHLESQK-RLWERFGHTQLELLDQRRIREVVACEEYVGGMLDMSG 180 L G + AA + L+ + RFG+ +L +D + V + Y+GG+ D Sbjct: 125 LTIGYLTAANKPRDTDALQKWRDEAQRRFGYDRLSYVDADGVGNYVQSQRYLGGLFDADS 184 Query: 181 GHIHPLNLALGEAAAVESLGGVIYEQS--PAVRIERGASPVVHTPQGKVRAKFIIVAGNA 238 GH+HPLN LG A A G I+E S A+R E G V T +G+V+A+F+++A N Sbjct: 185 GHLHPLNYTLGLARAAREAGVQIFEDSCVTALREEDGRH-VAETARGRVQARFVVLACNT 243 Query: 239 YLGNLVPELAAKSMPCGTQVIATEPLGDELAHSLLPQDYCVEDCNYLLDYYRLTGDKRLI 298 YLG L P++A K MP GT VIATEPL + A +L+P V D ++LDY+R D RL+ Sbjct: 244 YLGQLAPDVANKIMPVGTYVIATEPLDPDRAEALMPAKAAVCDSRFVLDYFRPAPDHRLL 303 Query: 299 FGGGVVYGARDPANIEAIIRPKMLKAFPQLKDVKIDYAWTGNFLLTLSRLPQVGRLGDNI 358 +GG V Y P N+ +R MLK FPQL DVKIDYAW G +T++R P GRL + Sbjct: 304 WGGKVSYSKLAPRNLGEAMRRDMLKTFPQLDDVKIDYAWGGFVDITMNRAPHFGRLSPTV 363 Query: 359 YYSQGCSGHGVTYTHLAGKVLAEALRGQAERFDAFADLPHYPFPGGQLLRTPFAAMGAWY 418 Y++QG SGHGV T LAGK++AEA+ GQA RFD F + H FPGG LRTP + + Sbjct: 364 YFAQGFSGHGVNTTGLAGKLIAEAIDGQASRFDLFGKIRHRDFPGGATLRTPALVLAMAW 423 Query: 419 YGLRD 423 Y ++D Sbjct: 424 YRMKD 428 Lambda K H 0.320 0.139 0.421 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 546 Number of extensions: 21 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 427 Length of database: 430 Length adjustment: 32 Effective length of query: 395 Effective length of database: 398 Effective search space: 157210 Effective search space used: 157210 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory